Over the long holiday weekend I noticed an interesting item in my twitter feed. A number of people were pointing to the post entitled: My Genome Via E-mail by David Ewing Duncan. Some of you may be familiar with David’s writing and his big project called “Experimental Man“. He has been exploring all sorts of biomedical tests and investigations about his body, making him probably the case of personalized medicine with the most depth at this point.
Well, he has also taken to genomics as part of this, of course. And now he’s one of the people in the Personal Genome Project and has his full genome sequence in hand. Well, sort of. He has it, but he’s asking for guidance on what to do with it:
This is an appeal: Send me you ideas for how best to interpret my newly sequenced complete genome!
Now, as an exercise over a year ago I thought this through. I have no expectation of having my genome any time soon–but it’s a question people ask me and I thought it was fun to think about. I reviewed that post the other day and I still think that’s what I’d do:
1) Assessment and QC
2) Build a personal genome browser with various tracks, including a literature track for personally curating stuff interesting or relevant to me
3) Look closer at specific medically relevant genes. I know this is looking under the flashlight, but the most knowledge and anything actionable would probably be in this set. I’d also look specifically into family issues (like that allergy/eczema stuff I found in my 23andMe data) and try to learn things there.
But I also thought I’d like to know what some of my peers in bioinformatics/genomics would do. As you may know if you follow this blog, we participate in discussions at BioStar. The participants here are active in genomics research around the world, and they are super-users of the tools of art in this field. Who better to ask? So I posted a question asking what they would do with their personal genome sequence. I offered my skeletal workflow as an example, and expected some thoughts on what they would do.
To my surprise, the top rated answer at this time says this:
I may be in minority but I’ll say this: right now I simply don’t want to know – Did you ever notice how genomic variation never correlates with good news. It seems there is only bad news. There are no SNPs for happiness, friendship or love….
Um. Ok. That’s one way to approach this. I was surprised, really–I didn’t expect the question to become philosophical. I really wanted a workflow.
For most of the weekend the second rated answer was this:
Whatever you do with it should be up to you to decide, use it for your personalized medicine if you wish. So my sole recommendation is: Keep the data private and well protected and encrypted! Decide in an informed way, whom you grant access to them….
There were real concerns about the security and misuse of this data.
There are a couple of other interesting answers as well. I have to say it was fascinating. It wasn’t what I expected–but it was illuminating for me. I haven’t always been the most enthusiastic participant in the personal genomics debate, as I have real concerns about security and misuse of the information, and the current utility. But it’s certainly coming whether we are ready or not, and I really wanted to know what people would do with it in a concrete way if they had it. And I thought bioinformatics/genomics professionals would have the best leads on this.
“right now I simply don’t want to know”
I’m considering adding a bounty to my question over there. You can add some of your own points to the question for encouragement to obtain an answer. And I’ll still be the highest ranked identified female over there–so I can afford the points.
If you have some thoughts and want to join BioStar, and if you give me a decent workflow, I may award the points to you! Anyone? Bueller? Bueller? Anyone?